Most riverine mangroves (characterized by salinity fluctuations and tidal inundations), are seriously threatened by metallic pollution. Whether differences in salinity and tidal effects along the river continuum can affect metallic bioaccumulation and the biomagnification of species is still unknown. Bivalves are representative sessile inhabitants in mangrove ecosystems, with a high capacity to bioaccumulate metallic contaminants. The present study used two bivalves, Meretrix lusoria and Mytilopsis sallei, to monitor inter-site changes in metallic contamination and assess the associated ecological impacts along the tidal gradients of riverine mangroves. The concentrations of a total of six metals (Cr, Ni, Cu, Zn, Cd and Pb) in M. lusoria and M. sallei, collected at three different sites along Danshuei Riverine Mangrove, were investigated. The metallic concentrations of the whole soft body of the studied bivalves, and the associated surface sediment from each site, were analyzed using inductively coupled plasma mass spectrometry (ICP-MS) to determine the inter-site effects on the bioaccumulation and biomagnification of metallic contaminants in bivalves. There are increasing concentrations of four metallic contaminants, Zn, Cr, Cd and Cu, in the seaward direction of the bivalves. The increasing mean metallic concentrations along the seaward direction may be the effect of salinity, further decreasing the rate of the elimination of these metals, thus resulting in a net increase in metallic contaminants. Our results clearly show prominent inter-site changes in the metallic burdens of bivalves in our study on riverine mangrove ecosystems associated with different levels of bioaccumulation and biomagnification of metallic contaminants. Thus, it is important to monitor multiple sites along the dynamic environment of riverine mangroves in order to gain a good understanding of the ecological impact of metallic pollution risks. The present findings provide important evidence of the use of simple indices to assess the ecological impacts of metallic pollution in riverine mangroves.